The purpose of the study was to examine the effects of progressively increased training intensity or volume on the nocturnal heart rate (HR) and heart rate variability (HRV), countermovement jump, perceived recovery, and heart rate-running speed index (HR-RS index). Another aim was to analyze how observed patterns during the training period in these monitoring variables were associated with the changes in endurance performance. Thirty recreationally trained participants performed a 10-week control period of regular training and a 10-week training period of either increased training intensity (INT, n = 13) or volume (VOL, n = 17). Changes in endurance performance were assessed by an incremental treadmill test. Both groups improved their maximal speed on the treadmill (INT 3.4 ± 3.2%, < 0.001; VOL 2.1 ± 1.8%, = 0.006). In the monitoring variables, only between-group difference ( = 0.013) was found in nocturnal HR, which decreased in INT ( = 0.016). In addition, perceived recovery decreased in VOL ( = 0.021) and tended to decrease in INT ( = 0.056). When all participants were divided into low-responders and responders in maximal running performance, the increase in the HR-RS index at the end of the training period was greater in responders ( = 0.005). In conclusion, current training periods of increased intensity or volume improved endurance performance to a similar extent. Countermovement jump and HRV remained unaffected, despite a slight decrease in perceived recovery. Long-term monitoring of the HR-RS index may help to predict positive adaptations, while interpretation of other recovery-related markers may need a more individualized approach.